Refinement of protein-protein complexes in contact map space with metadynamics simulations

Accurate protein-protein complex prediction, to atomic detail, is a challenging problem. For flexible docking cases, current state-of-the-art docking methods are limited in their ability to exhaustively search the high dimensionality of the problem space. In this study, to obtain more accurate models, an investigation into the local optimization of initial docked solutions is presented with respect to a reference crystal structure. We show how physics-based refinement of protein-protein complexes in contact map space (CMS), within a metadynamics protocol, can be performed. The method uses 5 times replicated 10 ns simulations for sampling and ranks the generated conformational snapshots with ZRANK to identify an ensemble of n snapshots for final model building. Furthermore, we investigated whether the reconstructed free energy surface (FES), or a combination of both FES and ZRANK, referred to as CS_α, can help to reduce snapshot ranking error.     

Dynamic properties of the fluxional Rh2H(μ-PPh2)2(PPh3)3 complex

The rhodium dimer [Rh₂H(PPh₂)₂(PPh₃)₃]⁻ was prepared from RhCl(PPh₃)₃ and K₄Sn₉ in the presence of 2,2,2-cryptand in ethylenediamine/toluene solvent mixtures. The [K(2,2,2-crypt)]⁺ salt was isolated and characterized via NMR and X-ray diffraction studies. The solid state structure reveals a binuclear, diphenylphosphido-bridged, 32 electron Rh(I)-Rh(I) complex with edge-shared tetrahedral and square planar Rh centers with overall C_s point symmetry. 1-D and 2-D ¹H, ³¹P, and ³¹P{¹H} NMR experiments were used to characterize the complex.     

Distribution of intramembranous particles and filipin-sterol complexes in the spermatid and spermatozoon of Culex quinquefasciatus (Culicidae).

A freeze-fracture study was carried out on spermatid and spermatozoon of the mosquito Culex quinquefasciatus. In the spermatid plasma membrane few and randomly distributed intramembranous particles were observed. In the spermatozoon the density of intramembranous particles was higher on the P- than on the E-fracture face of the plasma membrane. Two populations of particles were observed. Large particles (about 15 nm in diameter) are regularly arranged in double rows as a zipper-line, longitudinally oriented in relation to the main cell axis. These strands of particles were observed in the posterior head region, mainly associated with the E-fracture face. Filipin was used to analyse the presence and distribution of cholesterol in thin sections and freeze-fracture replicas. Filipin-sterol complexes were not homogeneously distributed throughout the spermatozoon plasma membrane. They were more abundant on the P-fracture face of the membrane lining the nuclear region. The results obtained show that Culex spermatozoon differs from those of other species in that its plasma membrane exhibits only a membrane domain, the zipper-line, localized in the postacrosomal region.     

Tunability of DNA Polymerase Stability during Eukaryotic DNA Replication

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Membranes of Rhodopseudomonas sphaeroides. VI. Isolation of a fraction enriched in newly synthesized bacteriochlorophyll a-protein complexes

Radioactivity eventually destined for the chromatophore membrane of Rhodopseudomonas sphaeroides was shown in pulse-chase studies to appear first in a distinct pigmented fraction. This material formed an upper pigmented band which sedimented more slowly than chromatophores when cell-free extracts were subjected directly to rate-zone sedimentation on sucrose density gradients. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that the purified fraction contained polypeptide bands of the same mobility as light-harvesting bacteriochlorophyll a and reaction center-associated protein components of chromatophores; these were superimposed upon cytoplasmic membrane polypeptides. The pulse-chase relation was confined mainly to the polypeptide components of these pigment-protein complexes. It is suggested that the isolated fraction may be derived from sites at which new membrane invagination is initiated.     

血清免疫炎症相关蛋白复合物、25-羟维生素D、脂肪细胞因子与炎症性肠病患者疾病活动性和肠道菌群的相关性研究

摘要 目的：探讨血清免疫炎症相关蛋白复合物（IIRPCs）、25-羟维生素D[25（OH）D]、脂肪细胞因子（Chemerin）与炎症性肠病（IBD）患者疾病活动性和肠道菌群的相关性。方法：选取2020年12月～2021年12月我院收治的150例IBD患者,其中溃疡性结肠炎（UC）组65例、克罗恩病（CD）组85例,另取同期健康体检者70例作为对照组,检测并比较三组血清IIRPCs、25（OH）D、Chemerin水平。此外,UC组和CD组患者分别根据克罗恩病活动指数（CDAI）和溃疡性结肠炎的改良梅奥（Mayo）评分分为活动期组、缓解期组,分别比较UC组和CD组患者活动期组与缓解期组间的血清IIRPCs、25（OH）D、Chemerin水平、肠道菌群差异,并作相关性分析。结果：IBD患者的血清IIRPCs、Chemerin水平高于对照组,而25（OH）D水平低于对照组（P＜0.05）;UC组血清IIRPCs、Chemerin水平高于CD组,25（OH）D水平低于CD组（P＜0.05）。活动期UC、CD患者的血清IIRPCs、Chemerin水平以及肠球菌、肠杆菌、酵母菌、拟杆菌数量均高于缓解期UC、CD患者,而血清25（OH）D水平以及双歧杆菌、乳酸杆菌数量均低于缓解期UC、CD患者（P＜0.05）。Pearsonn相关性分析结果显示,UC、CD患者的血清IIRPCs、Chemerin水平与肠球菌、肠杆菌、酵母菌、拟杆菌数量呈正相关,与双歧杆菌、乳酸杆菌数量呈负相关（P＜0.05）;UC、CD患者的血清25（OH）D水平与肠球菌、肠杆菌、酵母菌、拟杆菌数量呈负相关,与双歧杆菌、乳酸杆菌数量呈正相关（P＜0.05）。结论：血清IIRPCs、25（OH）D、Chemerin与IBD患者的疾病活动性、肠道菌群有关,检测上述指标对评估IBD患者病情程度有一定价值。     

Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling

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New tailored substituted benzothiazole Schiff base Cu(II)/Zn(II) antitumor drug entities: effect of substituents on DNA binding profile,antimicrobial and cytotoxic activity

New tailored Cu(II) & Zn(II) metal-based antitumor drug entities were synthesized from substituted benzothiazole o?vanillin Schiff base ligands. The complexes were thoroughly characterized by elemental analysis, spectroscopic studies {IR, ¹H & ¹³C NMR, ESI?MS, EPR} and magnetic susceptibility measurements. The structure activity relationship (SAR) studies of benzothiazole Cu(II) & Zn(II) complexes having molecular formulas [C₃₀H₂₂CuN₅O₇S₂], [C₃₀H₂₀Cl₂CuN₅O₇S₂], [C₃₀H₂₀CuF₂N₅O₇S₂], [C₃₀H₂₂N₄O₄S₂Zn], [C₃₀H₂₀Cl₂N₄O₄S₂Zn], and [C₃₀H₂₀F₂N₅O₇S₂Zn], with CT?DNA were performed by employing absorption, emission titrations, and hydrodynamic measurements. The DNA binding affinity was quantified by K _b and K _sv values which gave higher binding propensity for chloro-substituted Cu(II) [C₃₀H₂₀Cl₂CuN₅O₇S₂] complex, suggestive of groove binding mode with subtle partial intercalation. Molecular properties and drug likeness profile were assessed for the ligands and all the Lipinski’s rules were found to be obeyed. The antimicrobial potential of ligands and their Cu(II) & Zn(II) complexes were screened against some notably important pathogens viz., E. coli, S. aureus, P. aeruginosa, B. subtilis, and C. albicans. The cytotoxicity of the complexes [C₃₀H₂₀Cl₂CuN₅O₇S₂], [C₃₀H₂₀CuF₂N₅O₇S₂], [C₃₀H₂₀Cl₂N₄O₄S₂Zn], and [C₃₀H₂₀F₂N₅O₇S₂Zn] were evaluated against five human cancer cell lines viz., MCF?7 (breast), MIA?PA?CA?2 (pancreatic), HeLa (cervix) and Hep?G2 (Hepatoma) and A498 (Kidney) by SRB assay which revealed that chloro-substituted [C₃₀H₂₀Cl₂CuN₅O₇S₂] complex, exhibited pronounced specific cytotoxicity with GI₅₀ value of 4.8 μg/ml against HeLa cell line. Molecular docking studies were also performed to explore the binding modes and orientation of the complexes in the DNA helix.     

Synthesis and X‐ray diffraction study of a chiral bis‐phosphahelicene palladium (II) complex

As a complement to our previous studies on the development of a class of chiral phosphahelicenes, this article discloses the synthesis, spectroscopic, and structural characterizations of a new phosphahelicene transition metal complex. It demonstrates the ability of these hindered chiral ligands to coordinate Pd (II) in trans‐complexes Cl₂Pd(L*)₂. In the solid state, the complex adopts a C2‐symmetric arrangement with two ligands facing each other on the same face of the coordination plane. X‐Ray data highlight bending of the Pd (II) unit from the expected planar coordination geometry that might be due to a significant π‐π stacking effect between the central rings of two helical units.